In order to follow along with this session you will need Cytoscape, but you can also just watch the walkthrough if you can’t be bothered to install something.
We will walk through an example together then you are free to work through one example network visulization on either: - Cell-cell connectivity - Gene co-expression - Authorship network
The gene expression and sample information data were collected from the Gene Expression Omnibus (GEO), under study ID GSE4051. The coexpression weights are from a Weighted Gene Coexpression Netwrok Analysis ( WGCNA ). Only the 95 most variable genes were used for calculating coexpression. Genes were sorted into two coexpression clusters (turquoise and grey), which represent genes expressed with a similar pattern as cross samples.
Suggested network building: > - File -> Import -> Network from File -> gene_coexpression_edges.txt > - Label “fromNode” as the source for node connections and “toNode” as the target. > - File -> Import -> Table from File -> gene_coexpression_nodes.txt > - “nodeName” should automatically be the key to merge the edge and node tables. > - Under the Style tab and Node settings try Fill Color as “nodeAttr”. Try and match cluster name to actual color. > - Then layout so the grey and turquiose modules are seperate > - Find the clearest way to weight the edges by the coexpression weight (i.e transparency, color, width)